(a) The title of your question. The concept of coefficient of restitution is useful for macroscopic bodies, but not for microscopic bodies like atoms. The exception is those head-on collisions between atoms when no kinetic energy is lost (elastic collisions). The relative velocity of separation is then equal and opposite to the relative velocity of approach, so we could say that the c of r is 1.
(b) Suppose a helium atom (mass $m_{He}$) moving at velocity $u$ (much less than the speed of light) makes a head-on collision with a stationary sodium atom (mass $m_{Na}$) and excites it, giving it an extra internal energy $\Delta E$.
Using conservation of momentum we have
$$m_{He} u = m_{He} v_{He}+m_{Na} v_{Na}$$
in which $v_{He}$ and $v_{Na}$ are the velocities after the collision.
But because energy is conserved we also have
$$\tfrac{1}{2}m_{He} u^2 = \Delta E + \tfrac{1}{2}m_{He} v_{He}^2+\tfrac{1}{2}m_{Na} v_{Na}^2$$
Provided that $\tfrac{1}{2}m_{He} u^2 > \Delta E$ you can solve these equations for $v_{He}$ and $v_{Na}$.